/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.annotator.interfaces;

import htsjdk.variant.vcf.VCFInfoHeaderLine;
import htsjdk.variant.variantcontext.VariantContext;
import org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.PerReadAlleleLikelihoodMap;

import java.util.List;
import java.util.Map;

// TODO -- make this an abstract class when we move away from InfoFieldAnnotation
public interface ActiveRegionBasedAnnotation extends AnnotationType {
    // return annotations for the given contexts split by sample and then read likelihood
    public abstract Map<String, Object> annotate(final Map<String, PerReadAlleleLikelihoodMap> stratifiedContexts, final VariantContext vc);

    // return the descriptions used for the VCF INFO meta field
    public abstract List<VCFInfoHeaderLine> getDescriptions();
}